Question: Unusual Chipseq Data
2
gravatar for Jarus
8.6 years ago by
Jarus20
Jarus20 wrote:

HI, I am looking at some ChIPSeq data that is rather unusual. The forward and reverse read form deep thin stacks. Their width is mostly just above the read length of 75 bp. The 'peaks' (pseudo-peaks?) are distributed well across the mouse genome. Have any of you see this? What could be the reason? This experiment is investigating transcription factor binding ....

Thanks! Jarus

read peak-calling chip-seq • 1.4k views
ADD COMMENTlink written 8.6 years ago by Jarus20
1
gravatar for Sean Davis
8.6 years ago by
Sean Davis26k
National Institutes of Health, Bethesda, MD
Sean Davis26k wrote:

It sounds like you might have a problem with PCR duplicates. This might arise because of inadequate starting DNA, for example. A thorough QC evaluation and perhaps some forensic bioinformatics are probably warranted before proceeding with your analysis.

ADD COMMENTlink written 8.6 years ago by Sean Davis26k
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